OMIA:002149-9913 : Haplotype with homozygous deficiency HH6 in Bos taurus (taurine cattle)

Categories: Mortality / aging (incl. embryonic lethal)

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal recessive lethal

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2018

Species-specific symbol: HH6

History: Fritz et al. (2018) "adopted the nomenclature HH6 . . . to acknowledge the previous discoveries and molecular characterizations of the HH1 [OMIA:000001-9913], HH3 [OMIA:001824-9913], HH4 [OMIA:001826-9913], and HH5 [OMIA:001941-9913] embryonic lethal mutations. The HH6 haplotype and HH6 mutation studied in this article should not be confused with the haplotype provisionally named HH6 in Fritz et al. (2013), which was actually associated with the mutation causing complex vertebral malformation" [OMIA:001340-9913].

Mapping: Using the homozygous haplotype deficiency strategy, Fritz et al. (2018) mapped an autosomal recessive embryonic lethal trait to a 1.1Mb region on chromosome BTA16.

Molecular basis: Within the mapped candidate region (see Mapping section), Fritz et al. (2018) identified a likely causal variant as "an A-to-G transition at position 29,773,628 bp on chromosome 16 (g.29773628A>G; rs434666183)". The authors explained that "This A-to-G transition changes the initiator ATG (methionine) codon to ACG because the gene is transcribed on the reverse strand. . . . Initiation of translation at the closest in-frame Met codon would truncate SDE2 by 83 amino acids, including an 8-amino acid motif conserved among eukaryotes".

Breed: Holstein (black and white) (Cattle) (VBO_0000237).
Breeds in which the phene has been documented. (If a likely causal variant has been documented for the phene, see the variant table breeds in which the variant has been reported).

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
SDE2 SDE2 telomere maintenance homolog (S. pombe) Bos taurus 16 NC_037343.1 (29020714..29005211) SDE2 Homologene, Ensembl , NCBI gene

Variants

By default, variants are sorted chronologically by year of publication, to provide a historical perspective. Readers can re-sort on any column by clicking on the column header. Click it again to sort in a descending order. To create a multiple-field sort, hold down Shift while clicking on the second, third etc relevant column headers.

WARNING! Inclusion of a variant in this table does not automatically mean that it should be used for DNA testing. Anyone contemplating the use of any of these variants for DNA testing should examine critically the relevant evidence (especially in breeds other than the breed in which the variant was first described). If it is decided to proceed, the location and orientation of the variant sequence should be checked very carefully.

Since October 2021, OMIA includes a semiautomated lift-over pipeline to facilitate updates of genomic positions to a recent reference genome position. These changes to genomic positions are not always reflected in the ‘acknowledgements’ or ‘verbal description’ fields in this table.

OMIA Variant ID Breed(s) Variant Phenotype Gene Allele Type of Variant Source of Genetic Variant Reference Sequence Chr. g. or m. c. or n. p. Verbal Description EVA ID Year Published PubMed ID(s) Acknowledgements
990 Holstein (black and white) (Cattle) Abortion due to haplotype HH6 SDE2 start-lost Naturally occurring variant ARS-UCD1.2 16 g.29020700A>G c.2T>C p.(M1?) ENSBTAT00000016992.6:c.2T>C ENSBTAP00000016992.5:p.Met1? "This A-to-G transition changes the initiator ATG (methionine) codon to ACG because the gene is transcribed on the reverse strand. . . . Initiation of translation at the closest in-frame Met codon would truncate SDE2 by 83 amino acids, including an 8-amino acid motif conserved among eukaryotes" rs434666183 2018 29680649

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2024). OMIA:002149-9913: Online Mendelian Inheritance in Animals (OMIA) [dataset]. https://omia.org/. https://doi.org/10.25910/2AMR-PV70

References

Note: the references are listed in reverse chronological order (from the most recent year to the earliest year), and alphabetically by first author within a year.

2024 Khan, M.Y.A., Dai, D., Su, X., Tian, J., Zhou, J., Ma, L., Wang, Y., Wen, W., Zhang, Y. :
Multiplex fluorescent amplification-refractory mutation system PCR method for the detection of 10 genetic defects in Holstein cattle and its comparison with the KASP genotyping assay. Anim Genet , 2024. Pubmed reference: 38622758. DOI: 10.1111/age.13432.
2023 Ask-Gullstrand, P., Strandberg, E., Båge, R., Rius-Vilarrasa, E., Berglund, B. :
The effect of genetic defects on pregnancy loss in Swedish dairy cattle. J Dairy Sci , 2023. Pubmed reference: 37977438. DOI: 10.3168/jds.2023-24159.
Bengtsson, C., Stålhammar, H., Thomasen, J.R., Fikse, W.F., Strandberg, E., Eriksson, S. :
Mating allocations in Holstein combining genomic information and linear programming optimization at the herd level. J Dairy Sci , 2023. Pubmed reference: 37028963. DOI: 10.3168/jds.2022-22926.
2019 Kamiński, S. :
Missense mutation in SDE2 gene - new lethal defect transmitted into Polish Holstein-Friesian cattle. Pol J Vet Sci 22:627-630, 2019. Pubmed reference: 31560480. DOI: 10.24425/pjvs.2019.129974.
2018 Fritz, S., Hoze, C., Rebours, E., Barbat, A., Bizard, M., Chamberlain, A., Escouflaire, C., Vander Jagt, C., Boussaha, M., Grohs, C., Allais-Bonnet, A., Philippe, M., Vallée, A., Amigues, Y., Hayes, B.J., Boichard, D., Capitan, A., Fritz, S., Hoze, C., Rebours, E., Barbat, A., Bizard, M., Chamberlain, A., Escouflaire, C., Vander Jagt, C., Boussaha, M., Grohs, C., Allais-Bonnet, A., Philippe, M., Vallée, A., Amigues, Y., Hayes, B.J., Boichard, D., Capitan, A. :
An initiator codon mutation in SDE2 causes recessive embryonic lethality in Holstein cattle. J Dairy Sci 101:6220-6231, 2018. Pubmed reference: 29680649. DOI: 10.3168/jds.2017-14119.

Edit History


  • Created by Frank Nicholas on 20 Apr 2018
  • Changed by Frank Nicholas on 20 Apr 2018
  • Changed by Imke Tammen2 on 20 Jan 2023
  • Changed by Frank Nicholas on 10 May 2024